PATRIC Workshop Agenda – University of Florida

Published on 2015-07-10

AGENDA

Monday, July 13, 2015

8:30am            Register for PATRIC Account

9:00am            Overview of PATRIC www.patricbrc.org

9:30am            Assemble a Genome in PATRIC

  • Uploading reads and read libraries
  • Selecting assembly methods for comparison
  • Queuing jobs and retrieving results
  • Analyzing assembly output and comparisons
  • Genome Assembly

10:30am          Break

10:45am          Annotate a Genome in PATRIC Using RASTtk

  • Uploading or selecting contigs in workspace
  • Selecting genome metadata and annotation options
  • Queuing jobs and retrieving results
  • Previewing an annotated genome
  • Genome Annotation

12:00pm          Lunch

1:00pm           Comparative Genomics: Protein Families and Pathways

  • Selecting sets of genomes for a study
  • Comparing by region, genes, proteins
  • Comparing pathways
  • Visualizing with heatmap viewer and downloads
  • Acinetobacter Use Case

5:00pm            Day 1: Adjourn

Tuesday, June 16, 2015

9:00am            Metabolic Modeling in PATRIC

9:45                 Proteomic Comparison

  • Selecting genomes for a study
  • Visualization of compared genomes
  • Download and analysis of results
  • Proteome Comparison

10:30am         Break

10:45am          RNA-Seq Pipeline, Downloading Data into PATRIC and differential expression

12:00pm          Lunch

1:00pm            Exploring Genes Identified by RNA-Seq and transcriptomic analysis

5:00pm            Day 2: Adjourn